Binsanity-profile stuck

[math....@gmail.com]

Hi! 

I'm looking forward to running my data through BinSanity. I have done the install and tested it out with the example data. However, I seem to be getting stuck on the BinSanity-profile step when preparing my own data. I'm not sure if it is something wrong with the installation or with my data?

When I run the BinSanity-profile step the Subread steps starts, but finishes with this error:

Traceback (most recent call last):
File "/usr/local/bin/Binsanity-profile", line 168, in <module>
make_coverage(args.inputIds,args.outCov,args.outDirectory)
File "/usr/local/bin/Binsanity-profile", line 52, in make_coverage
contig_length = cov_data[k].pop(0)
IndexError: pop from empty list

The output files look to be empty. 

I'm not sure where to go from here.

Thanks,

Matt.
 

[Elaina Graham]

Hi Matt,

What command did you use to call Binsanity-profile?

It looks likes featureCounts isn't producing anything.

Regards,

Elaina

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[Elaina Graham]

Hi Matt,

I attempted to replicate this error, does Binsanity-profile fail to produce the `.saf` and `.readcounts` files? If so then likely what is happening is your BAM files aren't being detected therefore ultimately you run into an issue where your coverage profile is empty and nothing can be produced. 

Check to see if all of your BAM files end with the `.bam` suffix, then check to be sure that the directory indicated by `-s` is pointing to the right location.

Regards,

Elaina